Fig. 6
Human fetal chondrocyte identity is regulated at the epigenetic level. a Left panel: Chromatin state definitions (emission probabilities) for the 12 state ChromHMM model. Rows correspond to chromatin states. Columns correspond to chromatin state number, color code, candidate description and histone marks. Numbers in the histone mark columns show the frequency of occurrence of each mark in each chromatin state on the scale from 0 (white) to 100 (red). Right panel: Enrichment scores for chromatin states in genomic features. The first column shows the genome-wide percentage of occupancy for each state on the scale from 0 (white) to 100 (green). Subsequent columns show enrichments for CpG islands, Refseq annotated exons, genes, transcription ends sites (TES), transcription start sites (TSS), TSS + −2 kb regions and laminB1 domains. Each column is colored from 0 (white) to its maximum value (blue). The bottom row shows the baseline percentage of genomic territory occupied by each feature. b Enrichments of chromatin states from Fetal 17-weeks in TSS proximal regions (defined as TSS + −2 kb) of genes from different gene expression modules identified by WGCNA. The first column shows the baseline percentage occupied by each chromatin state in all annotated TSS + −2 kb regions on the scale from 0 (white) to 100 (green). Subsequent columns show the enrichments for each state in each expression module based on the fraction occupied by that state in the TSS proximal regions of all genes. Each column is colored from 0 (white) to its maximum value (blue). The bottom row shows the baseline fraction of each module out of all genes. Promoters of cartilage and ligament genes are enriched for active promoter states, whereas bone, muscle and tendon genes are enriching for Polycomb-repressed, poised and low signal states. c Chromatin data from all four cell types interrogated in this study and from H1-hESC at specific genes involved in either cartilage development (SOX9, COL2 and ACAN) or pluripotency (NANOG and DPPA4). ChromHMM tracks are colored according to the color codes in a. N = 3–4
